Advanced search - This page allows users to search and narrow down the AS locus which the users want to know by using following search items (Figure 1):
Figure 1. Screenshot of Advanced search.
Any combinations are available.
- RASV set & Locus/cDNA information - They are same as the simple search system on top page. RASV sets are derived from H-Inv full-length cDNAs, H-Inv all transcripts and Mouse full-length cDNAs. The items of Locus/cDNA information are keyword, H-Inv Transcript (HIT), H-Inv CluSter (HIX), Accession/RefSeq/ENST, HUGO gene symbol, Entrez Gene, OMIM, EC and definition;
- Genomic structure - Chromosome number, genome strand, genome position, splice-site sequences, ESE (RASVs of H-Inv full-length cDNAs only) and retrotransposons (RASVs of H-Inv full-length cDNAs only);
- AS genomic structure - Number of RASVs, AS location, AS pattern and AS initiation/termination;
- Functional annotation - ORF length, protein motif, GO, subcellular localization signal (Subcell) and transmembrane domain (TMD);
- AS functional annotation - Difference in length of encoded protein, AS relating CDS region, AS affecting protein function and complex AS pattern.
- Evolutionary conservation (RASVs of H-Inv full-length cDNAs only) - Exon level conservation (non-conserved, genome-conserved and transcript conserved) and transcript level conservation (non-conserved, genome-conserved, transcript conserved, ESV and conserved AS).
BLAST search - This page allows users to execute homology search for the nucleic acid and CDS sequences of RASV datasets.
AS Viewer - This is a Java applet to show the exon structure on genome, protein function and conservation with mouse about RASVs. It has also user-controllable function to investigate RASVs more carefully by operating it dynamically. AS Viewer consists of following parts (Figure 2A):
Figure 2A. Screenshot of AS Viewer.
- Annotation display controller of RASVs (Figure 2B) - This controller allows users to see several annotations of RASVs in the exon structure figure (iv). (i-1) Functional annotations such as protein motif and transmembrane domain are displayed in the upside of exons. (i-2) Conservation level with mouse analized by comparative genomics (RASVs of H-Inv full-length cDNAs only) and (i-3) ESE and retrotransposon (RASVs of H-Inv full-length cDNAs only) are displayed in the downside of exons;
Figure 2B. Annotation display controller of RASVs.
- Zoom and Structure mode - This functions allow users to operate the RASV size and structure figure. The user can see the nucleic and amino acid sequences of RASVs by clicking Zoom button and the RASV structures either without constitutive introns or with them by selecting Structure mode. In Genome view mode, the user can focus on the assigned genomic position;
- Display of AS pattern and location - This fugure is the assembled RASVs of the locus. AS patterns are indicated by different colors and 5'/3' AS exons are shown under the exons. Human genome is shown if the structure mode is genome;
- Exon structure of RASV - This is a main part of AS viewer. Exons and introns indicate squares and lines respectively. Users can operate the display of RASVs by using the checkbox in the left side. Users can also operate the order of RASVs by clicking arrow button after selecting a RASV. The green and yellow in exons show ORF and UTR respectively. Pop-up window appears by clicking exons. The background colors of RASVs indicate conserved AS and the corresponding mouse cDNAs have same color in the exon strucure figure of mouse (v) (H-Inv full-length cDNA dataset only). RefSeq, Ensembl and other ASVs in the AS group of RASV can be shown as reference sequences;
- Human-mouse genome alignment and mouse locus (Figure 2C) (H-Inv full-length cDNA dataset only) - Genomes of human and mouse indicate blue squares and aligned genomes are connected by aqua belts (v-1). Pop-up window appears by clicking the genome alignment. Exon structure fugure of mouse locus is a compliant to iv (v-2). Mouse genome is shown if the structure mode is genome (v-3);
Figure 2C. Human-mouse genome alignment and mouse locus.